Publications by authors named "Pascal Auffinger"

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Principles of ion binding to RNA inferred from the analysis of a 1.55 Å resolution bacterial ribosome structure - Part I: Mg2.
Filip Leonarski, Anja Henning-Knechtel, Serdal Kirmizialtin, Eric Ennifar, Pascal Auffinger

Nucleic Acids Res· January 2025

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RNA dynamics from experimental and computational approaches.
Giovanni Bussi, Massimiliano Bonomi, Paraskevi Gkeka, Michael Sattler, Hashim M Al-Hashimi, Pascal Auffinger

Structure· September 2024

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Multiscale Modeling of Phosphate···π Contacts in RNA U-Turns Exposes Differences between Quantum-Chemical and AMBER Force Field Descriptions.
Klaudia Mráziková, Holger Kruse, Vojtěch Mlýnský, Pascal Auffinger, Jiří Šponer

J Chem Inf Model· December 2022

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Lone Pair…π Contacts and Structure Signatures of r(UNCG) Tetraloops, Z-Turns, and Z-Steps: A WebFR3D Survey.
Craig L Zirbel, Pascal Auffinger

Molecules· July 2022

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Short-Range Imbalances in the AMBER Lennard-Jones Potential for (Deoxy)Ribose···Nucleobase Lone-Pair···π Contacts in Nucleic Acids.
Klaudia Mráziková, Jiří Šponer, Vojtěch Mlýnský, Pascal Auffinger, Holger Kruse

J Chem Inf Model· November 2021

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Deflating the RNA Mg bubble: stereochemistry to the rescue!
Pascal Auffinger, Eric Ennifar, Luigi D'Ascenzo

RNA· February 2021

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Short but Weak: The Z-DNA Lone-Pair⋅⋅⋅π Conundrum Challenges Standard Carbon Van der Waals Radii.
Holger Kruse, Klaudia Mrazikova, Luigi D'Ascenzo, Jiri Sponer, Pascal Auffinger

Angew Chem Int Ed Engl· September 2020

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Comment on "Evaluating Unexpectedly Short Non-covalent Distances in X-ray Crystal Structures of Proteins with Electronic Structure Analysis".
Holger Kruse, Jiri Sponer, Pascal Auffinger

J Chem Inf Model· September 2019

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Nucleobase carbonyl groups are poor Mg inner-sphere binders but excellent monovalent ion binders-a critical PDB survey.
Filip Leonarski, Luigi D'Ascenzo, Pascal Auffinger

RNA· February 2019

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Identification of receptors for UNCG and GNRA Z-turns and their occurrence in rRNA.
Luigi D'Ascenzo, Quentin Vicens, Pascal Auffinger

Nucleic Acids Res· September 2018

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Nucleic acid nanomaterials: Silver-wired DNA.
Pascal Auffinger, Eric Ennifar

Nat Chem· September 2017

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Revisiting GNRA and UNCG folds: U-turns versus Z-turns in RNA hairpin loops.
Luigi D'Ascenzo, Filip Leonarski, Quentin Vicens, Pascal Auffinger

RNA· March 2017

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Mg2+ ions: do they bind to nucleobase nitrogens?
Filip Leonarski, Luigi D'Ascenzo, Pascal Auffinger

Nucleic Acids Res· January 2017

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'Z-DNA like' fragments in RNA: a recurring structural motif with implications for folding, RNA/protein recognition and immune response.
Luigi D'Ascenzo, Filip Leonarski, Quentin Vicens, Pascal Auffinger

Nucleic Acids Res· July 2016

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Sodium and Potassium Interactions with Nucleic Acids.
Pascal Auffinger, Luigi D'Ascenzo, Eric Ennifar

Met Ions Life Sci· June 2016

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Anions in Nucleic Acid Crystallography.
Luigi D'Ascenzo, Pascal Auffinger

Methods Mol Biol· May 2016

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A comprehensive classification and nomenclature of carboxyl-carboxyl(ate) supramolecular motifs and related catemers: implications for biomolecular systems.
Luigi D'Ascenzo, Pascal Auffinger

Acta Crystallogr B Struct Sci Cryst Eng Mater· April 2015

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Protein capsules assembled via isobutyramide grafts: sequential growth, biofunctionalization, and cellular uptake.
Damien Mertz, Jiwei Cui, Yan Yan, Glyn Devlin, Christophe Chaubaroux, Pascal Auffinger

ACS Nano· September 2012

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Metal ion binding to RNA.
Pascal Auffinger, Neena Grover, Eric Westhof

Met Ions Life Sci· October 2011

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A short guide for molecular dynamics simulations of RNA systems.
Yaser Hashem, Pascal Auffinger

Methods· March 2009

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Spontaneous Formation of KCl Aggregates in Biomolecular Simulations: A Force Field Issue?
Pascal Auffinger, Thomas E Cheatham, Andrea C Vaiana

J Chem Theory Comput· September 2007

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Dinucleotide TpT and its 2'-O-Me analogue possess different backbone conformations and flexibilities but similar stacked geometries.
Guillaume P H Santini, Christophe Pakleza, Pascal Auffinger, Céline Moriou, Alain Favre

J Phys Chem B· August 2007

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Nucleic acid solvation: from outside to insight.
Pascal Auffinger, Yaser Hashem

Curr Opin Struct Biol· June 2007

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SwS: a solvation web service for nucleic acids.
Pascal Auffinger, Yaser Hashem

Bioinformatics· April 2007

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Halogen bonds in biological molecules.
Pascal Auffinger, Franklin A Hays, Eric Westhof, P Shing Ho

Proc Natl Acad Sci U S A· November 2004

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